54 lines
1.6 KiB
Python
54 lines
1.6 KiB
Python
import os
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import numpy as np
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import matplotlib.pyplot as plt
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import nixio as nix
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from IPython import embed
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def analyze_sams(filename):
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print(filename)
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f = nix.File.open(filename, nix.FileMode.ReadOnly)
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b = f.blocks[0]
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b.metadata.pprint(max_depth=-1) # max_depth=-1: alles rausschreiben
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print(b.groups)
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for g in b.groups:
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if 'sam' in g.name.lower():
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break
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rtag_data = g.tags[0]
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rtag_data.metadata.pprint(max_depth=-1)
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print(40*'*')
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stim_tag = g.multi_tags[0]
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stim_pos = stim_tag.positions[:] # beginnings of stimulations
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stim_extent = stim_tag.extents[:] # duration of stimulations
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for r in rtag_data.references:
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print(r.name, r.type)
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voltage_trace = rtag_data.references['V-1']
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spike_data = []
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for idx in range(len(stim_pos)):
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spike_data.append(stim_tag.retrieve_data(idx, 'Spikes-1')[:])
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# dims = [[]] * len(spike_data)
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# for j in range(len(spike_data)):
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# dims[j] = spike_data.dimensions[j]
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# print(spike_data, len(spike_data))
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# embed()
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# exit()
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f.close()
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return stim_pos, stim_extent, spike_data, voltage_trace
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if __name__ == '__main__':
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data_dir = '/home/lisa/data'
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data_set = '2019-06-24-aa-invivo-1'
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stim_pos, stim_extent, spike_data, voltage_trace = analyze_sams(os.path.join(data_dir, data_set, data_set + '.nix'))
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for i in range(len(stim_pos)):
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plt.scatter(voltage_trace.dimensions[i].axis(1000), spike_data[i][:1000])
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plt.show()
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# spikes = stim_tag.retrieve_data(i, 'Spikes-1')[:]
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# print(spikes)
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# embed()
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# exit() |